Hi there James!
Yes you can. By default the KNIME executable file (knime.exe) will look for a file beside the launcher with the same name and the extension .ini (knime.ini). One way to override this is to use --launcher.ini parameter. I tested it and started KNIME from Command Prompt with following syntax from KNIME installation folder:
start knime.exe --launcher.ini test/knime.ini
Maybe there is a cleaner solution (corporation like solution) for this 
Here is a link that helped me:
Br,
Ivan
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